Abhishek Tiwari:Bioinformatics Toolkits
Bioinformatics Toolkits
Geneious http://www.geneious.com/
Geneious(Free for academic use) provides sophisticated genome & proteome research tools, protein or molecular visualization, publication literature search and storage tools and more, with revolutionary usability.Plugins extend Geneious's functionality by providing additional document importers or exporters, document viewers, database access or operations such as alignment or tree building. Anyone can write plugins using our freely available Public API – in fact, most of Geneious's standard functionality is internally provided by plugins.
BioPerl www.bioperl.org
Bioperl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. As such, it does not include ready to use programs in the sense that many commercial packages and free web-based interfaces do (e.g. Entrez, SRS). On the other hand, Bioperl does provide reusable Perl modules that facilitate writing Perl scripts for sequence manipulation, accessing of databases using a range of data formats and execution and parsing of the results of various molecular biology programs including Blast, clustalw, TCoffee, genscan, ESTscan and HMMER. Consequently, bioperl enables developing scripts that can analyze large quantities of sequence data in ways that are typically difficult or impossible with web based systems.In order to take advantage of bioperl, the user needs a basic understanding of the Perl programming language including an understanding of how to use Perl references, modules, objects and methods.Bioperl is open source software that is still under active development.
BioJava http://biojava.org
BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It include objects for manipulating biological sequences, file parsers, DAS client and server support, access to BioSQL and Ensembl databases, tools for making sequence analysis GUIs and powerful analysis and statistical routines including a dynamic programming toolkit.
BioJava is used in several real-world bioinformatics applications and has been used for bioinformatics analysis in a number of published studies. For example Biosense a commercial informatics offering from Inforsense that uses BioJava under the hood.
BioPython http://biopython.org/
The Biopython Project is an international association of developers of freely available Python tools for computational molecular biology.Project develop reusable Python code for anything related to biology and computing.
